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Conserved domains on  [gi|1402624441|ref|NP_001351376|]
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Fanconi anemia group M protein homolog isoform 2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XPF_nuclease_FANCM cd20077
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
 1039-1176 3.11e-74

XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also called Fanconi anemia-associated polypeptide of 250 kDa (FAAP250), or protein Hef ortholog, or ATP-dependent RNA helicase FANCM, is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA) and Holliday junction substrates. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, FANCM strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA.


:

Pssm-ID: 410853 [Multi-domain]  Cd Length: 139  Bit Score: 242.56  E-value: 3.11e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1039 CILVDSREITTGLEVISSLRTVHGLQVEICPLNGCDYIVSSRMVVVRRSQSEMLSNTSKNKFIEQMQRLQSMFQRICVIV 1118
Cdd:cd20077      2 VILVDSREISSGQEVISSLRIKHGIKVEVCQLGGCDYIVSNRMGVERKSLSEFANGSNRSKLVERIQHLCDLYDRPCLII 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1402624441 1119 EKDREKAGDTSKKFRRTKCYDSLLTALVGAGIRILFSSGQEETADLLKELSLVEQRKN 1176
Cdd:cd20077     82 EKDRVKPGETSRIFHRTKYYDSTLAALAQAGVRVLFSDSQEETARLLADLAQLEQRKN 139
FANCM-MHF_bd super family cl25109
FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia ...
 1-29 4.50e-10

FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia complementation group protein M that binds to a two-histone-fold-containing protein complex MHF. MHF binds double-strand DNA, stimulates the DNA-binding activity of FANCM, and contributes to the targeting of FANCM to chromatin.


The actual alignment was detected with superfamily member pfam16783:

Pssm-ID: 465270  Cd Length: 116  Bit Score: 58.52  E-value: 4.50e-10
                           10        20
                   ....*....|....*....|....*....
gi 1402624441    1 MKMIEGMRHEEGECSYELKIRPFLQMEDV 29
Cdd:pfam16783   88 MEMIELMRQEEDECSYELELKPYLQMEDV 116
uvrC super family cl35109
excinuclease ABC subunit UvrC;
1185-1247 1.15e-03

excinuclease ABC subunit UvrC;


The actual alignment was detected with superfamily member PRK00558:

Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 43.18  E-value: 1.15e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1402624441 1185 LNTSKLEalpfylSIPGI--SYITALnmCHQFSSVKKMANSSPEEISTCAQVNHQKAEEIYKYIH 1247
Cdd:PRK00558   540 RLTSALD------DIPGIgpKRRKAL--LKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALH 596
 
Name Accession Description Interval E-value
XPF_nuclease_FANCM cd20077
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
 1039-1176 3.11e-74

XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also called Fanconi anemia-associated polypeptide of 250 kDa (FAAP250), or protein Hef ortholog, or ATP-dependent RNA helicase FANCM, is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA) and Holliday junction substrates. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, FANCM strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA.


Pssm-ID: 410853 [Multi-domain]  Cd Length: 139  Bit Score: 242.56  E-value: 3.11e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1039 CILVDSREITTGLEVISSLRTVHGLQVEICPLNGCDYIVSSRMVVVRRSQSEMLSNTSKNKFIEQMQRLQSMFQRICVIV 1118
Cdd:cd20077      2 VILVDSREISSGQEVISSLRIKHGIKVEVCQLGGCDYIVSNRMGVERKSLSEFANGSNRSKLVERIQHLCDLYDRPCLII 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1402624441 1119 EKDREKAGDTSKKFRRTKCYDSLLTALVGAGIRILFSSGQEETADLLKELSLVEQRKN 1176
Cdd:cd20077     82 EKDRVKPGETSRIFHRTKYYDSTLAALAQAGVRVLFSDSQEETARLLADLAQLEQRKN 139
PRK13766 PRK13766
Hef nuclease; Provisional
 1040-1246 8.15e-15

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 79.53  E-value: 8.15e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1040 ILVDSREITTGleVISSLRTvHGLQVEICPLNGCDYIVSSRMVVVRRSQSEML-SNTSKNKFiEQMQRLQSMFQRICVIV 1118
Cdd:PRK13766   565 IIVDSRELRSN--VARHLKR-LGAEVELKTLEVGDYVVSDRVAVERKTAEDFVdSIIDRRLF-EQVKDLKRAYERPVLII 640

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1119 EKDREKAGDTSKKFRRtkcyDSLLTALVGAGIRILFSSGQEETADLLKELSLVEQRKNAGihiPAVLNTSK----LEALP 1194
Cdd:PRK13766   641 EGDLYTIRNIHPNAIR----GALASIAVDFGIPILFTRDEEETADLLKVIAKREQEEEKR---EVSVHGEKkamtLKEQQ 713

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1402624441 1195 FYL--SIPGISYITALNMCHQFSSVKKMANSSPEEISTCAQVNHQKAEEIYKYI 1246
Cdd:PRK13766   714 EYIveSLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVV 767
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
 1042-1168 5.63e-14

ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.


Pssm-ID: 426945 [Multi-domain]  Cd Length: 139  Bit Score: 70.15  E-value: 5.63e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1042 VDSREITTGLEVISSLRtvHGLQVEICPLNGCDYIVSSR-----------MVVVRRSQSEMLSNTSKNKFIEQMQRLQSM 1110
Cdd:pfam02732    1 VDTRELRSSIPELLLEE--LGVEVVVETLPVGDYLWVPReydlelevvldVIVERKSLDDLVSSIIDGRLFEQKSRLKRG 78

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1402624441 1111 FQRICVIVE---KDREKAGDTSKKFRRTKCYDSLLTALVGAGIRILFSSGQEETADLLKEL 1168
Cdd:pfam02732   79 YKKPILLVEgldLFSRKLKNKRRDINPNAIEGALASLQVDYGVRIIRTRSAEETAEWLASL 139
ERCC4 smart00891
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, ...
 1039-1119 7.61e-12

ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.


Pssm-ID: 214888 [Multi-domain]  Cd Length: 98  Bit Score: 62.75  E-value: 7.61e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441  1039 CILVDSREITTGLE--VISSLRTVHGLQVEICPLNGCDYIVSSR-------------MVVVRRSQSEMLSNTSKNKFIEQ 1103
Cdd:smart00891    1 EIIVDSRELRSALEapIPRSLRWKRGVKVEYDRLEAGDFVLVARdkqsllphvnslnELVERKSLTDLVASIPDGRLFEQ 80

                            90
                    ....*....|....*..
gi 1402624441  1104 MQRL-QSMFQRICVIVE 1119
Cdd:smart00891   81 VRRLqQIAYPSPQLLVE 97
FANCM-MHF_bd pfam16783
FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia ...
 1-29 4.50e-10

FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia complementation group protein M that binds to a two-histone-fold-containing protein complex MHF. MHF binds double-strand DNA, stimulates the DNA-binding activity of FANCM, and contributes to the targeting of FANCM to chromatin.


Pssm-ID: 465270  Cd Length: 116  Bit Score: 58.52  E-value: 4.50e-10
                           10        20
                   ....*....|....*....|....*....
gi 1402624441    1 MKMIEGMRHEEGECSYELKIRPFLQMEDV 29
Cdd:pfam16783   88 MEMIELMRQEEDECSYELELKPYLQMEDV 116
rad1 TIGR00596
DNA repair protein (rad1); All proteins in this family for which functions are known are ...
 1040-1247 6.23e-10

DNA repair protein (rad1); All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273163 [Multi-domain]  Cd Length: 814  Bit Score: 63.68  E-value: 6.23e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1040 ILVDSREITTGLeviSSLRTVHGLQVEICPLNGCDYIVSSRMVVVRRSQSEMLSNTSKNKFIEQMQRLQSMFQRICVIVE 1119
Cdd:TIGR00596  589 VIVDMREFRSSL---PSLLHRRGIRVIPCMLTVGDYILTPDICVERKSISDLIGSLNNGRLYNQCEKMLRYYAYPVLLIE 665

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1120 KDREKA----------GDTSKKFRRTKCYDSLLTaLVGAGIRILFSSGQEETADLLKELSLVEQRKNA------GIHIPA 1183
Cdd:TIGR00596  666 FDQNKSfsleprndlsQEISSVNNDIQQKLALLT-LHFPKLRIIWSSSPYATAEIFEELKLGKEEPDPataaalGSDENT 744

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1402624441 1184 VLNTSKL--EALPFYLSIPGISYITALNMCHQFSSVKKMANSSPEEISTCAQvNHQKAEEIYKYIH 1247
Cdd:TIGR00596  745 TAEGLKFndGPQDFLLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNELIG-DEEAAKRLYDFLR 809
uvrC PRK00558
excinuclease ABC subunit UvrC;
1185-1247 1.15e-03

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 43.18  E-value: 1.15e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1402624441 1185 LNTSKLEalpfylSIPGI--SYITALnmCHQFSSVKKMANSSPEEISTCAQVNHQKAEEIYKYIH 1247
Cdd:PRK00558   540 RLTSALD------DIPGIgpKRRKAL--LKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALH 596
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
1187-1247 2.34e-03

Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 42.03  E-value: 2.34e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1402624441 1187 TSKLEalpfylSIPGISYITALNMCHQFSSVKKMANSSPEEISTCAQVNHQKAEEIYKYIH 1247
Cdd:COG0322    547 KSVLD------EIPGIGPKRRKALLKHFGSLKAIKEASVEELAAVPGISKKLAEAIYEYLH 601
 
Name Accession Description Interval E-value
XPF_nuclease_FANCM cd20077
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
 1039-1176 3.11e-74

XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also called Fanconi anemia-associated polypeptide of 250 kDa (FAAP250), or protein Hef ortholog, or ATP-dependent RNA helicase FANCM, is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA) and Holliday junction substrates. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, FANCM strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA.


Pssm-ID: 410853 [Multi-domain]  Cd Length: 139  Bit Score: 242.56  E-value: 3.11e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1039 CILVDSREITTGLEVISSLRTVHGLQVEICPLNGCDYIVSSRMVVVRRSQSEMLSNTSKNKFIEQMQRLQSMFQRICVIV 1118
Cdd:cd20077      2 VILVDSREISSGQEVISSLRIKHGIKVEVCQLGGCDYIVSNRMGVERKSLSEFANGSNRSKLVERIQHLCDLYDRPCLII 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1402624441 1119 EKDREKAGDTSKKFRRTKCYDSLLTALVGAGIRILFSSGQEETADLLKELSLVEQRKN 1176
Cdd:cd20077     82 EKDRVKPGETSRIFHRTKYYDSTLAALAQAGVRVLFSDSQEETARLLADLAQLEQRKN 139
XPF_nuclease-like cd19940
nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap ...
 1039-1170 3.74e-33

nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap endonuclease that act upon 3'-flap structures and involved in DNA repair pathways that are necessary for the removal of UV-light-induced DNA lesions and cross-links between DNA strands. Family members exist either as heterodimers or as homodimers in their functionally competent states which consist of a catalytic and a noncatalytic subunit. The catalytic subunits have a DX(n)RKX(3)D motif. This motif is required for metal-dependent endonuclease activity but not for DNA junction binding. The equivalent regions of the noncatalytic subunits (ERCC1, EME1, and FAAP24) have diverged. The noncatalytic subunits have roles such as binding ssDNA or an ability to target the endonuclease to defined DNA structures or sites of DNA damage.


Pssm-ID: 410849 [Multi-domain]  Cd Length: 126  Bit Score: 124.80  E-value: 3.74e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1039 CILVDSREIttGLEVISSLRTVhGLQVEICPLNGCDYIVSSRMVVVRRSQSEMLSNTSKNKFIEQMQRLQSMFQRICVIV 1118
Cdd:cd19940      1 SIVVDPRER--RSELLSELQRL-GVQVEFEDLAVGDYVLSNRTCVERKSLSDLVSSINKGRLREQLQRLTRKFERRVLLV 77

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1402624441 1119 EKDREKAGdtskKFRRTKCYDSLLTAL-VGAGIRILFSSGQEETADLLKELSL 1170
Cdd:cd19940     78 EKDRSKFR----SMVSSVQALSALTKLqLLTGIRLLIVASPKETADLLEELTQ 126
XPF_ERCC4_MUS81-like cd22367
XPF family DNA repair endonuclease; (Xeroderma Pigmentosum group F) DNA repair gene homologs ...
 1040-1165 3.77e-20

XPF family DNA repair endonuclease; (Xeroderma Pigmentosum group F) DNA repair gene homologs are members of the XPF/Rad1/Mus81-dependent nuclease family which specifically cleave branched structures generated during DNA repair, replication, and recombination, and they are essential for maintaining genome stability. They belong to a wider superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411771 [Multi-domain]  Cd Length: 123  Bit Score: 87.32  E-value: 3.77e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1040 ILVDSREITTGLEVISSLrtvHGLQVEICPLNGCDYIVSSRMVVVRRSQSEMLSNTSKNKFIEQMQRLQSMFQRICVIVE 1119
Cdd:cd22367      1 IVVDSRERRSGLPELLRK---LGVRVEVRTLEVGDYILSADIIVERKTVSDLISSIIDGRLFEQAERLKRSYERPILLIE 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1402624441 1120 KDREKAGDTSKKFRRTKCYDSLLTALvgaGIRILFSSGQEETADLL 1165
Cdd:cd22367     78 GDPDKARRLVRPAALGAAISSLLVIG---GLLVLRTPNFETTALLL 120
PRK13766 PRK13766
Hef nuclease; Provisional
 1040-1246 8.15e-15

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 79.53  E-value: 8.15e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1040 ILVDSREITTGleVISSLRTvHGLQVEICPLNGCDYIVSSRMVVVRRSQSEML-SNTSKNKFiEQMQRLQSMFQRICVIV 1118
Cdd:PRK13766   565 IIVDSRELRSN--VARHLKR-LGAEVELKTLEVGDYVVSDRVAVERKTAEDFVdSIIDRRLF-EQVKDLKRAYERPVLII 640

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1119 EKDREKAGDTSKKFRRtkcyDSLLTALVGAGIRILFSSGQEETADLLKELSLVEQRKNAGihiPAVLNTSK----LEALP 1194
Cdd:PRK13766   641 EGDLYTIRNIHPNAIR----GALASIAVDFGIPILFTRDEEETADLLKVIAKREQEEEKR---EVSVHGEKkamtLKEQQ 713

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1402624441 1195 FYL--SIPGISYITALNMCHQFSSVKKMANSSPEEISTCAQVNHQKAEEIYKYI 1246
Cdd:PRK13766   714 EYIveSLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVV 767
XPF_nuclease_XPF_arch cd20075
nuclease domain of XPF found in archaea; XPF, also called DNA excision repair protein ERCC-4, ...
 1040-1168 2.32e-14

nuclease domain of XPF found in archaea; XPF, also called DNA excision repair protein ERCC-4, or DNA repair protein complementing XP-F cells, or Xeroderma pigmentosum group F-complementing protein, is a 3'-flap repair endonuclease that cleaves 5' of ds/ssDNA interfaces in 3' flap structures, although it also cuts bubble, Y-DNA structures and mobile and immobile Holliday junctions. XPF cuts preferentially after pyrimidines, may continue to progressively cleave substrate upstream of the initial cleavage, at least in vitro. It may be involved in nucleotide excision repair. The nuclease domains of the catalytic subunits XPF have the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity but not for DNA junction binding. XPF-ERRC1 and its yeast homolog Rad1-Rad10 play key roles in the excision of DNA lesions and are required for certain types of homologous recombination events and for the repair of DNA cross-links.


Pssm-ID: 410851 [Multi-domain]  Cd Length: 127  Bit Score: 70.88  E-value: 2.32e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1040 ILVDSREitTGLEVISSLRTvHGLQVEICPLNGCDYIVSSRMVVVRRSQSEMLSNTSKNKFIEQMQRLQSMFQRICVIVE 1119
Cdd:cd20075      2 IIVDSRE--KNSGVVRELKE-LGVEVEFKQLEVGDYIVSDRVAIERKTVDDFVSSIIDGRLFDQAKRLKEAYEKPILIIE 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1402624441 1120 kdrekaGDTSKKFRRTK---CYDSLLTALVGAGIRILFSSGQEETADLLKEL 1168
Cdd:cd20075     79 ------GDLLYLKRRIHpnaIRGALASIALDFGIPIIFTKDPEETAELLYSL 124
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
 1042-1168 5.63e-14

ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.


Pssm-ID: 426945 [Multi-domain]  Cd Length: 139  Bit Score: 70.15  E-value: 5.63e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1042 VDSREITTGLEVISSLRtvHGLQVEICPLNGCDYIVSSR-----------MVVVRRSQSEMLSNTSKNKFIEQMQRLQSM 1110
Cdd:pfam02732    1 VDTRELRSSIPELLLEE--LGVEVVVETLPVGDYLWVPReydlelevvldVIVERKSLDDLVSSIIDGRLFEQKSRLKRG 78

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1402624441 1111 FQRICVIVE---KDREKAGDTSKKFRRTKCYDSLLTALVGAGIRILFSSGQEETADLLKEL 1168
Cdd:pfam02732   79 YKKPILLVEgldLFSRKLKNKRRDINPNAIEGALASLQVDYGVRIIRTRSAEETAEWLASL 139
ERCC4 smart00891
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, ...
 1039-1119 7.61e-12

ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.


Pssm-ID: 214888 [Multi-domain]  Cd Length: 98  Bit Score: 62.75  E-value: 7.61e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441  1039 CILVDSREITTGLE--VISSLRTVHGLQVEICPLNGCDYIVSSR-------------MVVVRRSQSEMLSNTSKNKFIEQ 1103
Cdd:smart00891    1 EIIVDSRELRSALEapIPRSLRWKRGVKVEYDRLEAGDFVLVARdkqsllphvnslnELVERKSLTDLVASIPDGRLFEQ 80

                            90
                    ....*....|....*..
gi 1402624441  1104 MQRL-QSMFQRICVIVE 1119
Cdd:smart00891   81 VRRLqQIAYPSPQLLVE 97
FANCM-MHF_bd pfam16783
FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia ...
 1-29 4.50e-10

FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia complementation group protein M that binds to a two-histone-fold-containing protein complex MHF. MHF binds double-strand DNA, stimulates the DNA-binding activity of FANCM, and contributes to the targeting of FANCM to chromatin.


Pssm-ID: 465270  Cd Length: 116  Bit Score: 58.52  E-value: 4.50e-10
                           10        20
                   ....*....|....*....|....*....
gi 1402624441    1 MKMIEGMRHEEGECSYELKIRPFLQMEDV 29
Cdd:pfam16783   88 MEMIELMRQEEDECSYELELKPYLQMEDV 116
rad1 TIGR00596
DNA repair protein (rad1); All proteins in this family for which functions are known are ...
 1040-1247 6.23e-10

DNA repair protein (rad1); All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273163 [Multi-domain]  Cd Length: 814  Bit Score: 63.68  E-value: 6.23e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1040 ILVDSREITTGLeviSSLRTVHGLQVEICPLNGCDYIVSSRMVVVRRSQSEMLSNTSKNKFIEQMQRLQSMFQRICVIVE 1119
Cdd:TIGR00596  589 VIVDMREFRSSL---PSLLHRRGIRVIPCMLTVGDYILTPDICVERKSISDLIGSLNNGRLYNQCEKMLRYYAYPVLLIE 665

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402624441 1120 KDREKA----------GDTSKKFRRTKCYDSLLTaLVGAGIRILFSSGQEETADLLKELSLVEQRKNA------GIHIPA 1183
Cdd:TIGR00596  666 FDQNKSfsleprndlsQEISSVNNDIQQKLALLT-LHFPKLRIIWSSSPYATAEIFEELKLGKEEPDPataaalGSDENT 744

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1402624441 1184 VLNTSKL--EALPFYLSIPGISYITALNMCHQFSSVKKMANSSPEEISTCAQvNHQKAEEIYKYIH 1247
Cdd:TIGR00596  745 TAEGLKFndGPQDFLLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNELIG-DEEAAKRLYDFLR 809
uvrC PRK00558
excinuclease ABC subunit UvrC;
1185-1247 1.15e-03

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 43.18  E-value: 1.15e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1402624441 1185 LNTSKLEalpfylSIPGI--SYITALnmCHQFSSVKKMANSSPEEISTCAQVNHQKAEEIYKYIH 1247
Cdd:PRK00558   540 RLTSALD------DIPGIgpKRRKAL--LKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALH 596
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
1187-1247 2.34e-03

Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 42.03  E-value: 2.34e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1402624441 1187 TSKLEalpfylSIPGISYITALNMCHQFSSVKKMANSSPEEISTCAQVNHQKAEEIYKYIH 1247
Cdd:COG0322    547 KSVLD------EIPGIGPKRRKALLKHFGSLKAIKEASVEELAAVPGISKKLAEAIYEYLH 601
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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